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leonarski_fandClaude Opus 5.5 aca27be862 jfjoch_writer writes rugnux's .mtz, _maps.mtz and _model.cif from the END blocks 
New gemmi-only library JFJochRugnuxFiles (writer/), linked by JFJochWriter, so
the writer needs no analysis library and builds with JFJOCH_WRITER_ONLY:
- WriteMergedMtz / WriteMapCoefficientsMtz / PlacedModelStructure make the
  files from the structured blocks; WriteRugnuxResultFiles writes whichever
  blocks END carries beside the master, each under a temporary name and renamed
  into place, an existing file replaced only when the run's overwrite is set.
  A file that fails costs only itself (logged), not the run.
- FillRugnuxResultBlocks reads the blocks back from the files rugnux wrote at
  a prefix (p.mtz, p_maps.mtz, p_model.cif), for the broker to fill END.

WriteMtzReflections now goes through WriteMergedMtz (MergedReflectionsForWriter
builds the block); its output is byte-identical to before, checked by md5 on a
synthetic set in both the Friedel-merged and the anomalous layout.

StreamWriter writes the files after the master and before the END ACK, so the
ACK means they are in place; END receipt and each rename are logged at INFO
with the wall-clock time, for last-frame-to-files latency. The broker's direct
HDF5 pusher writes them too.

Test: rugnux's three files -> blocks -> CBOR -> writer reproduces all of them
(and _model.pdb) byte for byte; a ~25k-reflection END is 2.7 MB.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-17 12:19:51 +02:00
..
crystfel
v1.0.0.rc-161 (#71)
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data
v1.0.0-rc.173 (#83)
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test_data
v1.0.0-rc.160 (#70)
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xds
v1.0.0-rc.175 (#85)
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xds_durin
v1.0.0-rc.175 (#85)
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xds_neggia
v1.0.0-rc.175 (#85)
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AcquisitionCountersTest.cpp
v1.0.0-rc.36
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AdaptiveSpotFinderCPUTest.cpp
v1.0.0-rc.173 (#83)
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AdaptiveSpotFinderGPUTest.cpp
v1.0.0-rc.175 (#85)
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AdaptiveThresholdTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
AnisotropyAnalysisTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
AutoIncrVectorTest.cpp
v1.0.0-rc.139 (#49)
2026-04-29 09:50:50 +02:00
AzimuthalIntegrationTest.cpp
v1.0.0-rc.173 (#83)
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BackgroundGainTest.cpp
v1.0.0-rc.175 (#85)
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BandwidthEstimateTest.cpp
v1.0.0-rc.175 (#85)
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BeamCenterFFTGPUTest.cpp
v1.0.0-rc.175 (#85)
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BeamCenterFFTTest.cpp
v1.0.0-rc.175 (#85)
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BeamCenterFromBackgroundTest.cpp
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
BearerTokensTest.cpp
v1.0.0-rc.173 (#83)
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BraggIntegrationEngineCompressedImageTest.cpp
1.0.0-rc.174 (#84)
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BraggIntegrationEngineCPUTest.cpp
v1.0.0-rc.175 (#85)
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BraggIntegrationEngineGPUTest.cpp
1.0.0-rc.174 (#84)
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BraggIntegrationEngineMetalTest.cpp
v1.0.0-rc.175 (#85)
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BraggStencilTest.cpp
1.0.0-rc.174 (#84)
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BrokerHttpAuthTest.cpp
v1.0.0-rc.175 (#85)
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BSLZ4DecoderGPUFuzzTest.cpp
v1.0.0.rc-161 (#71)
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BSLZ4DecoderGPUTest.cpp
v1.0.0.rc-161 (#71)
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CalcBraggPredictionTest.cpp
v1.0.0-rc.175 (#85)
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CalibrationTest.cpp
v1.0.0-rc.166 (#76)
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CBORTest.cpp
v1.0.0-rc.173 (#83)
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CCTest.cpp
v1.0.0-rc.146 (#56)
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CheckImageOutput.h
v1.0.0-rc.36
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CMakeLists.txt
jfjoch_writer writes rugnux's .mtz, _maps.mtz and _model.cif from the END blocks
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CoordTest.cpp
v1.0.0-rc.41
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CorrectionSurfaceGPUTest.cpp
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
CrystalLatticeTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
CrystalSettingTest.cpp
v1.0.0-rc.173 (#83)
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CudaHandledErrorTest.cpp
v1.0.0-rc.175 (#85)
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CUDAMemHelpersTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
DectrisSimplonClientTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
DetectorGeometryTest.cpp
v1.0.0-rc.103 (#8)
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DetectorSettingsTest.cpp
v1.0.0-rc.139 (#49)
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DetectorSetupTest.cpp
v1.0.0.rc-162 (#72)
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DetGeomCalibTest.cpp
v1.0.0-rc.166 (#76)
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DiagnosticOutputTest.cpp
v1.0.0-rc.175 (#85)
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DiffractionExperimentTest.cpp
v1.0.0-rc.166 (#76)
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DiffractionGeometryTest.cpp
v1.0.0-rc.166 (#76)
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DiffractionSpotTest.cpp
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DirectHostReadGPUTest.cpp
v1.0.0-rc.175 (#85)
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enospc_shim.c
SHIM library improvements from the HDF Group
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FPGAFrameGeneratorTest.cpp
version 1.0.0-rc.25
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FPGAHLSModulesTest.cpp
v1.0.0-rc.91
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FPGAHostWriterTest.cpp
v1.0.0-rc.34
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FPGAIntegrationTest.cpp
v1.0.0-rc.97
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FPGANetworkTest.cpp
v1.0.0-rc.72
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FPGAPTPTest.cpp
v1.0.0-rc.72
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FPGASpotFindingUnitTest.cpp
v.1.0.0-rc.32
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FrameTransformationTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
FrenchWilsonTest.cpp
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
GoniometerAxisTest.cpp
v1.0.0-rc49
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GridScanSettingsTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
HDF5WritingTest.cpp
HDF5Writer_Socket: wait for the subscription before the first file is announced
2026-10-17 09:06:54 +02:00
HistogramTest.cpp
v1.0.0-rc.121 (#28)
2025-12-12 21:24:20 +01:00
HKLKeyTest.cpp
v1.0.0-rc.124 (#31)
2026-02-01 13:29:33 +01:00
HotPixelFinderTest.cpp
v1.0.0-rc.175 (#85)
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ImageBufferTest.cpp
v1.0.0-rc.128 (#35)
2026-03-03 22:24:44 +01:00
ImageMetadataTest.cpp
v1.0.0-rc.103 (#8)
2025-11-19 09:40:50 +01:00
ImagePreprocessorGPUFusedTest.cpp
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
ImageSpotFinderCPUTest.cpp
v1.0.0-rc.173 (#83)
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ImageSpotFinderGPUTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
IndexingUnitTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
JFCalibrationTest.cpp
v1.0.0-rc.36
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JFConversionTest.cpp
version 1.0.0-rc.25
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jfjoch_hdf5_enospc_test.cpp
v1.0.0.rc-162 (#72)
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JFJochReaderTest.cpp
v1.0.0-rc.175 (#85)
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JFJochReceiverIntegrationTest.cpp
v1.0.0-rc.150 (#60)
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JFJochReceiverLiteTest.cpp
v1.0.0-rc.173 (#83)
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JFJochReceiverPlotsTest.cpp
v1.0.0-rc.153 (#63)
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JFJochReceiverProcessingTest.cpp
v1.0.0-rc.160 (#70)
2026-07-19 09:39:28 +02:00
JFJochStateMachineTest.cpp
v1.0.0-rc.169 (#79)
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JFPedestalTest.cpp
version 1.0.0-rc.25
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JPEGTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
LatticeReductionTest.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
LatticeSearchTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
LePageLatticeTest.cpp
v1.0.0-rc.167 (#77)
2026-09-09 07:25:13 +02:00
LiveCollectionTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
LoadReferenceMtzFreeFlagsTest.cpp
v1.0.0-rc.173 (#83)
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LoadReferenceSfCifTest.cpp
v1.0.0-rc.173 (#83)
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LossyFilterTest.cpp
version 1.0.0-rc.25
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MergeScaleTest.cpp
v1.0.0-rc.175 (#85)
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ModelMaskGPUTest.cpp
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ModelScaleGPUTest.cpp
v1.0.0-rc.175 (#85)
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ModelScalingTest.cpp
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ModelValidationTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
ModuleSummationTest.cpp
version 1.0.0-rc.27 minor fixes
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MolecularReplacementTest.cpp
v1.0.0-rc.175 (#85)
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MovingAverageTest.cpp
v1.0.0-rc.31
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MultiLatticeSearchTest.cpp
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
nxmx_geometry_dials_test.py
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
PairSortGPUTest.cpp
v1.0.0-rc.175 (#85)
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ParallelForTest.cpp
v1.0.0-rc.175 (#85)
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PedestalCalcTest.cpp
v1.0.0-rc.97
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PixelMaskTest.cpp
v1.0.0.rc-161 (#71)
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PortableTest.cpp
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PostRefineTest.cpp
v1.0.0-rc.175 (#85)
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PreflightTest.cpp
v1.0.0-rc.165 (#75)
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PreviewCounterTest.cpp
version 1.0.0-rc.25
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RawToConvertedGeometryTest.cpp
v1.0.0-rc.97
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ReceiveRingBufferTest.cpp
v1.0.0-rc.175 (#85)
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RegressionTest.cpp
1.0.0-rc.89
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ReindexAmbiguityTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
ResolutionShellsTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
ResultReportTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
RfreeFlagsTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
RingsFromProfileTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
ROIIntegrationCPUTest.cpp
v1.0.0-rc.153 (#63)
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ROIIntegrationGPUTest.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
ROIMapTest.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
RotationIndexerTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
RotationIngestGPUTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
RotationScaleWalkTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
RugnuxLargeTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
RugnuxResultFilesTest.cpp
jfjoch_writer writes rugnux's .mtz, _maps.mtz and _model.cif from the END blocks
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RugnuxTest.cpp
v1.0.0-rc.175 (#85)
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SearchSpaceGroupTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
SearchSpaceGroupTwinTest.cpp
v1.0.0-rc.169 (#79)
2026-09-15 17:09:31 +02:00
ShadowFinderTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
SphericalHarmonicSurfaceTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
SpindleBlindFractionTest.cpp
v1.0.0-rc.167 (#77)
2026-09-09 07:25:13 +02:00
SpindleCuspLossTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
SpotExtractorGPUParityTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
SpotFootprintTest.cpp
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
SpotTilesTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
SpotUtilsTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
StatusVectorTest.cpp
v1.0.0-rc.127 (#34)
2026-03-02 15:57:12 +01:00
StoredImageDecodeGPUTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
StreamWriterTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
StrongPixelSetTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
SweepLayoutTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
SyntheticMergedReflections.h
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
TCPImagePusherTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
TestData.h
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
ThreadSafeFIFOSetTest.cpp
v1.0.0-rc.135 (#44)
2026-04-16 11:59:59 +02:00
TIFFTest.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
TimeTest.cpp
v1.0.0-rc.96 (#1)
2025-11-02 13:45:57 +01:00
TopPixelsTest.cpp
v1.0.0-rc.121 (#28)
2025-12-12 21:24:20 +01:00
TranslationalNCSTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
TwinningAnalysisTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
UnitCellTest.cpp
v1.0.0-rc.146 (#56)
2026-05-28 18:48:35 +02:00
WilsonOutliersTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
WriteReflectionsTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
XDSPluginTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
XtalOptimizerTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
XtalRefineCeres.h
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
XtalRefineTest.cpp
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
ZMQImagePusherTest.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
ZMQMetadataSocketTest.cpp
v1.0.0-rc.133
2026-03-26 20:50:33 +01:00
ZMQPreviewSocketTest.cpp
version 1.0.0-rc.25
2024-11-22 21:25:20 +01:00
ZSTDCompressorTest.cpp
v1.0.0-rc.173 (#83)
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